Since cardiac structuring dimensions inform surgical decisions making, Z-score systematic error impairs surgical decision making and confounds outcome measurement, hence a similar error may affect the Nakata index. In this study, PubMed was searched using the terms: "pulmonary," "artery," "size," "Nakata," "Fontan," and "outcome". Studies that did not describe the outcome of the Fontan procedure and the size of the branch pulmonary arteries were excluded. Outcome measures of interest, in relation to BPA size, included: Operative mortality, Fontan "take-down", length of ICU stay, pleural effusions and functional capacity. The results revealed that of 116 papers retrieved, 9 were included representing 1,042 patients who underwent the Fontan procedure. Six out of 9 papers representing 645 (61.9%) patients reported that BPA size had no relationship with the outcome of the Fontan procedure; while 2 out of 9 papers representing 366 (35.1%) patients found that BPA size did affect the outcome. One paper representing 31 (3%) patients was unable to find any relationship. All the papers that concluded that there was no relationship labelled normal sized BPAs as small because of a systematic error introduced by the Nakata index. Papers that found a relationship did not use the Nakata index. Thus, Nakata index systematic error may impair surgical decision making and confound outcome measurement in Fontan surgery. In addition, continued use of the Fontan index may have similar implications for other congenital heart lesions.